Epigenetic regulation and function of imprinted genes

The National Institute of General Medical Sciences awarded $478,621 to The Trustees of The University of Pennsylvania on April 1, 2026, under the Biomedical Research and Research Training program (CFDA 93.859, Assistance Listing R35GM161389) to conduct basic research elucidating the epigenetic regulation and function of imprinted genes in mammals.

The recipient will investigate the mechanisms by which parental identity of imprinted genes is established, maintained, and reprogrammed in the germline, with specific focus on the H19/IGF2 and GRB10/DDC1A imprinted domains. Work includes study of CTCF-binding imprinting control regions that regulate imprinting, DNA methylation establishment in the male and female germline, maintenance of methylation patterns after fertilization during genome-wide reprogramming, and TET1-mediated active DNA demethylation during germline reprogramming. The recipient will employ genetically modified mice and cell lines to discover mechanisms for germline establishment and maintenance of imprinting marks and will investigate species-specific sequences and epigenetic machinery involved in these processes. The research is intended to inform understanding of Beckwith-Wiedemann syndrome, Silver-Russell syndrome, and other human disorders where imprinting defects determine disease transmission.

Performance occurs in Philadelphia, Pennsylvania, with a period of performance from April 1, 2026, through March 31, 2031.

Abstract

A few hundred genes in mammals are regulated by genomic imprinting. These genes are epigenetically marked and exhibit parental-of-origin-specific gene expression. Imprinting plays a role in the transmission of a number of human disorders, including beckwith-wiedemann syndrome and silver-russell syndrome, where the SEX of the parent transmitting the affected gene(s) determines whether offspring will be impacted. Additionally, imprinted genes are primarily responsible for the block to uniparental development, highlighting the importance of precise dosage and function of these genes during development. Our work aims to elucidate the mechanism(s) by which parental identity of imprinted genes is established, maintained and reprogrammed in the germline. In-depth study of imprinted genes will further inform our understanding of genome regulation and nuclear architecture, as imprinted genes are located in large domains and are often regulated by long non- coding rnas, ctcf-dependent insulators, and allele-specific epigenetic modifications. We will focus on the H19/IGF2 and GRB10/DDC1A imprinted domains, both of which harbor ctcf-binding imprinting control regions (icrs) that regulate imprinting. H19/IGF2 and GRB10/DDC1A also represent imprinted clusters with DNA methylation at icrs conferred in the male and female germline, respectively. Using genetically modified mice and cell lines, we aim to discover the mechanism(s) for germline establishment of DNA methylation at icrs and its subsequent maintenance after fertilization when the majority of the genome is reprogrammed. This work will also contribute to a better understanding of critical species-specific sequences and epigenetic machinery involved in these processes. Additionally, we will investigate the mechanism of TET1-mediated active DNA demethylation during germline reprogramming for imprints and other sequences. We recently developed TET1 catalytic variant mutants to dissect the requirement for non-catalytic activity and iterative oxidation of 5-methylcytosine by TET enzymes in vivo. Using these newly derived variants, we will elucidate TET1-dependency of icrs and other sequences in the female germline. Additionally, we intend to identify TET1-interacting proteins in the germline to illuminate further the role of active DNA demethylation during germline reprogramming. Finally, we will investigate how male and female gametes with methylation defects due to TET1 mutation led to mid-gestation lethality. Together, our work will deepen our understanding of epigenetic regulation and reprogramming during mammalian development.